That's kind of a re-invention of history. CM simply didn't integrate pdroid because it was a support nightmare waiting to happen. At the time of the pdroid discussion, Steve said that they were already working on a bunch of privacy features that would meet the usability standards they were aspiring to... and here we are.
Don't forget that this message encryption follows on from the App Privacy Mode that they have successfully deployed since then (and makes much of pdroid redundant). They are taking a measured and transparent approach to privacy. Just as a serious organisation should..